Abstract Convective overturning arising from static instability during winter is thought to play a crucial role in the formation of North Atlantic Deep Water (NADW). In ocean general circulation models (OGCMs), a strong reduction in convective penetration depth arises when horizontal diffusion (HD) is replaced by Gent and McWilliams (GM) mixing to model the effect of mesoscale eddies on tracer advection. In areas of sinking, the role of vertical tracer transport due to convection is largely replaced by the vertical component of isopycnal diffusion along sloping isopycnals. Here, the effect of this change in tracer transport physics on the stability of NADW formation under freshwater (FW) perturbations of the North Atlantic (NA) in a coupled model is examined. It is found that there is a significantly increased stability of NADW to FW input when GM is used in spite of GM experiments exhibiting consistently weaker NADW formation rates in unperturbed steady states. It is also found that there is a significant increase in NADW stability upon the introduction of isopycnal diffusion in the absence of GM. This indicates that isopycnal diffusion of tracer rather than isopycnal thickness diffusion is responsible for the increased NADW stability observed in the GM run. This result is robust with respect to the choice of isopycnal diffusion coefficient. Also, the NADW behavior in the isopycnal run, which includes a fixed background horizontal diffusivity, demonstrates that HD is not responsible in itself for reducing NADW stability when simple horizontal diffusion is used. Our results suggest that care should be taken when interpreting the results of coarse grid models with regard to NADW sensitivity to FW anomalies, regardless of the choice of mixing scheme.